At the beginning of May 1941, potential recruits for the Einsatzgruppen gathered in the Border-Police School in Pretsch on the River Elbe, northeast of Leipzig. Due to lack of space, some were accommodated in Duben and Bad-Schmiedberg. There, similar units were organized and prepared for the occupation of the Balkans, the Soviet Union and even for Operation Sea-Lion, the invasion of Britain.

There were no specific instructions as to who should be sent to Pretsch, and the RSHA manpower section turned to various departments of the SIPO and SD in its search for candidates. A large contingent from the Berlin-Charlotenburg SIPO Senior Commanders School, as well as 100 Kripo (Kriminalpolizel, or Criminal Police) cadets, were also assigned there.

The commanders of the Einsatzgruppen and Einsatzkommandos were chosen by Himmler and Heydrich from a list compiled by the RSHA Department One. Of the 75 selected, 42 were members of the SD. In addition to Sipo and SD officers, a support staff of drivers, translators, radio operators and clerks was also assembled.

These latter came from all over Germany, though most were members of the SS. Some were conscripted in accordance with the emergency law of 1938. Three of the Einsatzgruppen were reinforced by companies from the 9th Police Reserve Battalion.

In Pretsch, companies from the Waffen SS Battalion for Special Duties set up from the First SS Infantry Battalion were attached to Einsatzkommando 9 and Sonderkommando 4a. (Waffen-SS were drawn from the Wehrmacht.) Later, pursuant to Himmler's directive of July 27, 1941, other units received similar reinforcements.

The Einsatzgruppen were attached to the commanders of the rear army groups by June 25, 1941, and had to send forward subunits to join the staff of the Higher SS stationed at the groups' headquarters.

Thus, Einsatzgruppe A, headed by SS-Standartenfuhrer (Colonel) Dr. Walter Stachlecker, joined Army Group North in Danzig; Einsatzgruppe B, headed by SS Brigadefuhrer (General) Arthur Nebe joined Army Group Center in Malo Yaroslavets. Einsatzgruppe C, headed at the time by SS Brigadefuhrer Dr. Otto Rasch, attached to Army Group South at Kiev. Einsatzgruppe D, headed by SS-Standartenfuhrer Professor Otto Ohlendorf, joined the headquarters of the Eleventh Army in Piatra-Meamt (Romania) on July 4, 1941.

Notably, the Einsatzgruppen included many high-ranking officers, intellectuals and lawyers. Otto Ohlendorf, who commanded Einsatzgruppe D, had earned degrees from three universities and achieved a doctorate in jurisprudence. One of the commanders of Einsatzgruppe C, Ernst Biberstein, was a Protestant pastor, theologian and church official.